Well, I
greatly appreciate everyone's comments but now I'm even more confused.
I had originally started thinking I'd book someplace in Ginza (CY Ginza isn't available, was considering CY Toyko Station), then was looking at the Westin, then the Hilton
Shinjuku, then the
Hyatt Centric but when I was looking at Hyatt, I noticed that the Hyatt Regency is available and I can book a Club level room with lounge access for fewer points than the Centric (and it looks like the HR is serviced by the airport bus but the CY and Centric are not).
Then I went back to look at the Hilton
Shinjuku again, but it looks like the points increased since I last checked and I don't have enough for a room there with lounge access (although if I decide on the Hilton, I can just get the Amex for gold status). Lounge access isn't a dealbreaker, but it's nice to have a place for a light breakfast, beverages and maybe a snack in the evening and I've really grown accustomed to taking advantage of it, especially when I'm traveling by myself for an extended period and have a night or two where I just don't feel like heading out to dinner alone.
Sandeep1 , I hear you about the transportation. I'm a native New Yorker and have been taking mass transit my entire life but I know getting around Toyko will be a challenge (already I'm struggling to understand all the different lines, I'm so used to places like NY, London and Paris where it's all one transit system). When I travel, I'm usually pretty good about doing my research and targeting the area where I want to be, but I think I'm feeling overwhelmed with all the options.
I also still have to figure out Kyoto, where I have two different Marriott choices (Westin and Ritz-Carlton) and neither seem to be that well-located, which is my issue with most of the available Marriott choices I have in Toyko. I may need to broaden my search there as well but would like to get Tokyo sorted out first and I'm really struggling with making a decision.