I've stayed at both places several times, and I like them both -- there are some distinct advantages to each.
The best part abot the Pen, for me, is that it offers a respite from the hustle and frenzy of Bangkok. The little boat ride across the river is refreshment for the mind, and it is pleasant to look out from your room over the river. The downside of the Pen is that nothing is within walking distance -- unless you're going to one of the hotel restaurants and bars, you'll need to take a taxi or a boat before you can use your legs.
The Hyatt is its own oasis in the middle of the city. The rooms are nicely designed, though not as spacious as the Pen and maybe not quite as luxe. (The Pen has a tv and hands-free telephone in the bathtub, for example, and the Hyatt does not.) The Hyatt has a great pool area and decent, if awkwardly laid-out, spa. The best feature is surely its location, right at the Gaysorn shopping center, within an easy walk of several other shopping areas, and directly at the Skytrain station.
I believe these to be two of the best places to stay in Bangkok. If I were going to be in the city for 6 days, I'd likely split my time between the two.