Most of the Shinjuku hotels you mentioned are clustered in the Skyscraper District (west side of Shinjuku station) whereas the major department stores (of which there are several) are South and East of the train station. It's a pretty good hike between the two but there are lots of things to see/buy in between. The boulevards in Shinjuku can make it seem like a long walk so, if you must although not really advantageous, you can take the subway between the two.

Same goes for Ginza except that I would say the shops are closer together and the department stores are smaller but clustered together as well. Most Ginza hotels (incl. the Renaissance) are on the edge of the district which means a nice walk (again, lost of things to see/buy along the way) to get around. Many subway lines intersect at Ginza which makes it very convenient.

Tokyo is like one giant shopping city divided into shopping districts. Most districts have huge department stores to go with their Oxford-St-like shopping streets but invariably, every district has a distinct shopping area. Within those districts, everything is within reasonable walking distance. To move from one district to another (which you should for variety and to experience the tsunami of humanity in Tokyo's subway), you should take the subway. Taxis are prohibitively expensive. The meter starts at Y660 (!) and everytime it ticks, it goes up by Y80 (!!). It's a coronary-inducing exercise watching the meter go. Subways are easier to navigate and easier on your wallet as well.

If you can, try not to limit yourself to just Ginza and Shinjuku. Shibuya has a great shopping area and very popular with foreigners and Roppongi Hills is the latest and greatest in Tokyo's ambition to be a vertical city.

Prices in Tokyo are astounding compared to Singapore and HK. I would probably load up on souvenirs and stuff in the latter two before I arrive at the former. Tokyo is, indeed, very safe. I don't think I encountered a seedy area in Tokyo and I felt safe walking around at night (except for the pushy touts in Roppongi who are annoying but harmless - part of the experience, I guess ).

Tokyo will reward the adventurous, so bring your best walking shoes and explore away!