They both have their ups and downs.
Sniper Rifle: 24 shots maximum, 4 shots per clip, can shoot fairly fast
Beam Rifle: 20 shots maximum, unlimited shots per "clip", if shot too fast in a row it will need time for re-charge
I voted for the Beam Rifle because of the lack of reload and if you're patient, the wait before you can shoot without it zapping you isn't very long. I also prefer the no-scope cross-hair.