The Japanese macro scene is huge, and generally beer to the Japanese just means Sapporo or Kirin, sometimes Asahi or Suntory. Although craft beer is present in Japan it is not as readily accessible as in the likes of the US. Generally in a bar or restaurant the vast, vast majority of the time there will not necessarily be a craft option available. For that, you need to hunt out one of the craft bars or brew pubs. Although they are reasonably numerous the issue is that Tokyo is so huge that you will need to make your own call on whether it's worth your while making the trek to particular places. Getting a few connections and then walking somewhere can take a while. Think of it a bit like London - if you're staying near St Pauls you might easily make a trip to Soho but you'd be unlikely too really good to far away just for a pub.
General comments-
I've been to a few different Baird taprooms (Yokohama and Harajuku) and they're good fun, but they're a real first wave brewer at this point.
Popeye is a bit of a mecca and I would recommend it. The Aldgate is another one which makes the top lists but did not impress as much.
Something you may want to be aware of is that in Japan sometimes the food and drink hubs in a particular area are actually the depatchika - department store food halls. In Ireland we would probably not intuitively assume this to be the case but in Japan the depachika often contain the really high-end stuff. You can pick up some serious bargains if you shop around closing time - boxed sets of sushi that must be sold by end of day, for example. They're also sometimes the best place to track down cans and bottles of Japanese craft breweries, if you can't make it to some of the specialist off licences. You can pick up a good range of cans fairly cheaply that might allow you to sample more stuff than trekking to craft beer bars.
The Golden Gai area in Shinjuku is a kind of touristy thing to do but I'd still recommend it. Mainly macro beers available but I tend to drink more whisky when in Japan frankly. Eat at Naga ramen restaurant when there.
I'd strongly recommend having a phone with google maps that you can access over there. The Japanese address system is a disaster and just relying on a paper map or written directions will often go wrong, and you cannot count on a Japanese being able to help you. When I started going to Japan in the 90s even fewer people spoke a bit of English and there was less bilingual signage, but it remains the case that the street layouts and address system means even Japanese struggle to find places sometimes. You can walk the same three blocks looking for a tiny place and then realise you need to be looking three levels up as well, 1st and 2nd floor restaurants and bars are not uncommon.
Enjoy, it's one of the definitive food and drink destinations in the world for my money.
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