I visited Tokyo on a business trip for a week in mid-March 2000. I didn't have much spare time for birding, but I managed to fit some in on the day of arrival (heavily jet-lagged), part of the next day and then an hour or so each morning near my hotel. I used Mark Brazil's "A Birdwatcher's Guide to Japan" (1987), which was an excellent if slightly out of date guide. It has a number of sites in central Tokyo (I could only manage a few), and I also checked out the area around my hotel. The only field guide I could get was "Wild Birds of Japan", the recently published photographic guide. The photos and small captions are all you need, but it's a pity it's not in English yet.
Jungle Crows were common, and I saw my first in one of the main streets in the centre of the city. A walk around Hibaya Park in mid-afternoon brought flocks of Tree Sparrows (strange to think they are now uncommon in the UK) and a few Brown-eared Bulbul, Great Tit, White Wagtail and Grey Starlings. A small pond held a couple of Mallards and several Spot-billed Duck. A section of moat around the Imperial Palace held several Little Grebes, a pair of Shovelers, more Spot-billed Duck and a Great Cormorant and three Mute Swans. A Black Kite flew high overhead mobbed by crows.
The Hama Rikyu (Detached Palace) Garden would probably have given me more birds if I had not arrived so late in the afternoon. Still, it was the only place where I saw Teal, Little Egret and Daurian Redstart, and there were also Mallard, Pochard, Tufted Duck, Black-headed Gulls, White Wagtail, Brown-eared Bulbul, Great Tit, Dusky Thrush and many Jungle Crows.
The Meiji shrine was an excellent site. Jungle Crows were abundant and Japanese Pygmy Woodpeckers were easy to pick out once I got my ear in for their calls. On the paths around the main shrine I saw Brown-eared Bulbul, Grey Wagtail, both Pale and Dusky Thrushes, a pair of Japanese White-eyes, Great Tit, Varied Tit, Tree Sparrow, Oriental Greenfinch and a Hawfinch. Around 20 Mandarin Duck were on the north pond, with 10 Mallard, 4 Spot-billed Duck and a Little Grebe. The Iris Garden had a small entrance fee (which may have explained the lack of people) but it gave me Oriental Turtle-doves, Great Tits and Tree Sparrows literally at my feet, a close view of a Japanese Bush Warbler, and single Varied Tit, Pale Thrush and Grey Wagtail.
The Shinobazu Pond at Ueno Park was a bit out of the way for me and did not have any birds I did not see elsewhere. The wildfowl do allow close approach though. I saw Little Grebe, Great Cormorant, Pintail, Pochard, Tufted Duck, Shoveler, Mallard, Spot-billed Duck, Black-headed Gull, Feral Pigeon, Brown-eared Bulbul, Jungle Crow and Tree Sparrow.
I stayed in a modern hotel near the Tokyo "Big Sight" convention centre in Ariake. This is on reclaimed land in Tokyo Bay about 20 minutes train ride from the centre. Although seemingly devoid of "wild" areas, I did make some good finds. A Dusky Thrush was resident in a small clump of trees immediately outside the hotel, until these were bulldozed on the third day! The open grass areas usually had a few Feral Pigeons and Grey Starlings. A walk at breakfast around Ariake tennis courts gave a handful of Azure-winged Magpies in the surrounding trees, as well as Brown-eared Bulbul and Oriental Turtle-dove.
An early morning walk around the waterfront at nearby Odaiba-kaihinkoen was a good choice. A singing Sky Lark was on rough ground near the Tokyo Teleport station. The waterfront park had Feral Pigeon, White Wagtail, Dusky Thrush, Brown-eared Bulbul, Jungle Crow, Grey Starling, Tree Sparrow and Oriental Greenfinch. The small bay held a pair of Great Crested Grebes, a large number of Greater Scaup, a few Pintail and Pochard, a pair of Tufted Duck, some Spot-billed Duck, many Common, Black-headed and Herring Gulls, and a single Slaty-backed Gull. A tree-covered island in the distance had lots of Grey Herons and Great Cormorants.
I travelled to see the shrine in the outskirts of the city one morning, about a 2-hour journey from my hotel by train. This forested site may well be productive, but by mid-morning there were a lot of people around and my list was correspondingly small. It did give me my first views of Varied Tit and Pale Thrush, and my only sighting of a Siberian Meadow Bunting. Other birds were Oriental Turtle-dove, Jungle Crow (many), Brown-eared Bulbul, Great Tit and Feral Pigeon. From a birding perspective it was probably not worth the time, since I saw all but the bunting in town, but the shrine is stunning and it is a nice place to visit.
I travelled on foot and on the tube. You can pay the cheapest fare and then settle the difference at a machine at your destination station, so tube travel is easy and very efficient (you don't need to understand Japanese since all station names are in English). The hardest part was finding the right exit in some of the larger stations. A visitors guide to Tokyo is a good idea, although you can get a "welcome pack" including a useful map from the information desk at Narita airport.
Little Grebe Tachybaptus ruficollis
Great Crested Grebe Podiceps cristatus
Great Cormorant Phalacrocorax carbo Grey Heron Ardea cinerea
Little Egret Egretta garzetta
Mute Swan Cygnus olor
Mandarin Duck Aix galericulata
Common Teal Anas crecca
Mallard Anas platyrhynchos
Spot-billed Duck Anas poecilorhyncha
Northern Pintail Anas acuta
Northern Shoveler Anas clypeata
Common Pochard Aythya ferina
Tufted Duck Aythya fuligula
Greater Scaup Aythya marila
Black Kite Milvus migrans
Common Gull Larus canus
Herring Gull Larus argentatus
Slaty-backed Gull Larus schistisagus
Black-headed Gull Larus ridbundus
Feral Pigeon Columba livia
Oriental Turtle-dove Streptopelia orientalis
Japanese Pygmy Woodpecker Picoides kizuki
Sky Lark Alauda arvensis
Grey Wagtail Motacilla cinerea
White Wagtail Motacilla alba
Brown-eared Bulbul Hypsipetes amaurotis
Daurian Redstart Phoenicurus auroreus
Dusky Thrush Turdus naumanni
Pale Thrush Turdus pallidus
Japanese Bush Warbler Cettia diphone
Great Tit Parus major
Varied Tit Parus varius
Japanese White-eye Zosterops japonica
Jungle Crow Corvus macrorhynchos
Azure-winged Magpie Cyanopica cyana
Grey Starling Sturnus cineraceus
Tree Sparrow Passer montanus
Oriental Greenfinch Carduelis sinica
Hawfinch Coccothraustes coccothraustes
Siberian Meadow Bunting Emberiza cioides