I have a 3D. I really enjoy it. Both phones are great choices. Go to the Sprint store, play with them a lot. Take your time. This is 2 years of your money. Only you can make the best choice. I will happily answer any questions regarding the 3D if you have any. Fans of both phones will tell you the phone they own is the best, but remember what is best for them may not be the best for you.
I have a Photon, and it seems like a nice phone. It's the only Android phone I've owned, though, so I can't really tell you how they compare. But I gather that the 3D has the prettier screen and the prettier interface, and the Photon has longer battery life and is easier to read in full sunlight.
I agree with newboyx, play with both, and see how you like the look and feel.
You need to stop by the store and play with them both. By asking this question you'll get those who favor the 3D and those who favor the Photon. AC has some excellent reviews on each device. Take the reviews and personal use of the phone in store to be the deciding factor. Remember you do have a return policy to exchange it for another device...
Have you considered the recently announced Epic 4G Touch?
That's great. Let us know how the phone goes for you. I seriously considered getting the Photon last month when my eligibility was open but decided to wait because of the recent device announcements and things I've got planned in life this month