Can you post the hotels you can choose from, and most importantly what you plan to do while in Taipei? Without it, it's difficult to give you good advice but in general, if it's between the three hotels mentioned:
Sheraton (MRT Shandao Temple)
The reason this hotel is there is because of the neighboring government buildings but this area has nothing particularly interesting for a tourist to do there. It is rather nondescript and in the evening becomes quite desolate. As I would usually choose a hotel based on its location, I'd advise against staying there.
Hyatt (Xinyi Planned Area, Taipei 101)
Next to the landmark Taipei 101. This area has been planned as the most presentable part of Taipei, and is full of shopping malls and department stores, which are all fine but look exactly like their counterparts anywhere else in the world. If you stay there, you'll enjoy it but you'll not be experiencing much of the real Taipei, which is arguably why you're travelling to Taipei in the first place. Another caveat is that the area and especially the flagship Taipei 101 mall with the very decent food court is overrun by tour groups from China, which very often makes the experience unbearable for anyone else, although Chinese package tourism is on the decrease now due to political factors, so perhaps it won't be so much of an issue by the time you come. Still, a very decent choice to stay overall. If you grow tired of the city you can do a short trail to climb the nearby Elephant Mountain.
Mariott (MRT Jiannan Rd, Miramar)
This is another recently developed area, which is unlike nearly anywhere else in Taipei. The Miramar shopping mall is not as grandiose as the Taipei 101 but it has its style, and the food court is nice as well. Both the crowds and the shopping options are more local here. There is a Ferris wheel with a very pleasant overlook on Taipei. This is also a good starting point for a riverside cycling trip (there is a public bike rental system with stations everywhere but for pleasure you want to cycle along the rivers). This area is served by the brown MRT line, which is completely elevated, and a great way to quickly see a lot of Taipei (sit in front of the first car, there is no driver, so the view is unobstructed), although it might be problematic if you travel with a lot of luggage during the rush hours. This place is calmer than the Taipei 101 area. I'm fairly certain if you stay there you'll be enjoying it as well.
That being said, if I were not constrained by the choice of hotels, I'd choose yet another area to stay, most likely Ximending. But of course it all depends on what you want to see and do.
Hope the above helps a little.