Where are your favorite Izakaya's in Tokyo for late night food and drinks with good atmosphere? I am staying in Shinagawa. Preferably around the Yamanote-Line (like shibuya, shinjuku, etc) close to the train station exits
I like Wattaribozu in Gotanda, although the menu might be difficult if you don't read Japanese (or even if you do). Here's my write-up for more info: http://bento.com/rev/0821.html
Tsukada Nojo in Shinagawa has excellent chicken dishes and a fun atmosphere, but last order is 10:30pm: http://www.bento.com/rev/3939.html
Shinagawa: As far as chain izakayas go, Warayakiya is a solid choice. It specialises in straw grilled katsuo (bonito) and chicken dishes, so counter seats in front of the grill offer plenty of Instagram moments. They have a nice selection of junmai sake - mostly from the Shikoku region. L.O. 11pm and 4am on Fridays.
An English review of their Roppongi shop.
Gotanda: Soregashi is an excellent sake specialist izakaya, that specialises in jizake and plates of rusticwashoku fare. No English menu, but to get around any language issues you could ask your hotel to request one of the course menus (¥3,000-¥5,000) which include sake pairings. L.O. 2am, and 3am on Fridays.
Meguro: Yakitori Sasaya is a place to enjoy a few drinks with some flavourful sticks and plates. They have a basic English menu. L.O.11:30pm.
Ebisu: Ippo is a cheap and cheerful spot with which service standard izakaya fare. They have a fairly comprehensive sake list, and an English speaking staff member who can help guide your selection. L.O. 2am.
Shibuya: Uoshin is a fish specialist izakaya chain with shops in Ebisu and Shibuya - my preference is the Shibuya Honten. Consistently good and consistently packed - so you'll need to book a few days ahead. L.O. 11:30pm
Mugen is a friendly robataya-yaki style izakaya, which is located in the hipster heartland of Udagawacho (10 minutes walk from Shibuya Station). They are used to foreign diners with no Japanese ability, so ordering won't be a problem. They've got a nice selection of well regarded brands on their sake menu too: Kokuryu, Hiroki, Jikon, Taka, Kuheiji... a much better range than your average izakaya. L.O. 12am.
Nakamura is a more stylish, upmarket option. Great food, thoughtful jizake selection and excellent service. They have a basic English menu, but you'll need to enquire about the daily specials. L.O. 11pm.
Was in Sasaya the other day. It's a solid "modern" yakitori-ya. Their pride points are bits like liver, heart, sunagimo, etc. Good stuff. I like the staff too, including the straight from manga type main guy.
I think this would make a decent choice for tourists. It seems a few grades up from a typical neighborhood place. They don't get many foreign guests they said but they do indeed have the skewer portion of menu in English. They asked me to check it. I think it's accurate but was a little googly eyed at that point...They were saying last order from 11pm.