Yeah, this is my department. If you wanna buy floppies monthly/weekly, there are a couple (very expensive) options, but Blister Comics in Akihabara is your best bet. They have the widest selection in Tokyo by far. They get weekly stuff shipped, and they have a large selection of trade paperback stuff. They even have back issues, like your typical comic shop in the West. Also, they do Free Comic Book Day, like the West, so make sure to go early on that day (the line is insane otherwise).
As you said, there's Kinokuniya. I thought that the one in Shinjuku towards Kabukicho was the one with the greatest selection, but if I recall correctly, they gave all their American comic stock to an associated shop on the first floor in another building. It may not be so great anymore.
The Mandarake in Shibuya with that is several floors down and seems kinda creepy—do you know the one I'm talking about? They have a decent and cheap selection of trades.
Your most fun option to look at older stuff is going to 神保町, which is just one of the most fun places in town generally. There are several bookstores with comics here. I believe the best one is called @ワンダー (アットワンダー may also come up on google maps). Their stock changes pretty regularly, and their prices are probably the most reasonable.
The sad truth in Japan is that your best option for saving money and finding what you want is going digital. If you have a tablet and the app Comixology, you can read everything at the same price (and due to sales, often times cheaper) than if you were in an English speaking nation that commonly sold comics. I highly recommend this route, because you are not going to be happy with the money you spend on imported comics, especially if you buy floppies each week.
If you absolutely must get physical, then I recommend importing through instocktrades.com. They sell most of their comics at 30-40% off. You may have to pay for international shipping, but you will still save a ton overall. The books also arrive in perfect condition, I've heard from many.
Happy hunting.
