It will depend on your personal preference and what you'd like to have in your tank.
My tank is predominately LPS and Softies. I've had 36" over my 90 gallon, with 48" Reefbrite LED's on each side in the past. There would be shadowing on the ends of the aquarium with this setup. However, some like it that way for placement of lower light corals on the ends. I personally like the spread of T5 from end to end, so currently I have a T5/LED hybrid with 48" ATI T5 and 2 Kessil AP700's.
If you search the threads, you'll see lots of pics of various setups.
I'd go with 48" as well; going shorter only limits you going forward. If you find you have too much light (highly unlikely), you can decrease the intensity of the LEDs. LPS and softies will adjust to higher light levels; just because we tend to provide less light to those corals doesn't mean they cant use or adjust to higher levels.