Besides eyeballing it and comparing the line to the seat tube, are there any tricks to getting 48 splined crank arms perfectly aligned? I must have spent a solid 15 minutes looking at them from every angle until I was satisfied.
If your bearings are decent, just take the non-drive pedal off and let the pedal weight pull the other side down, or slowly let it fall from slightly off center. This is how I could tell with my Bullseye cranks, besides hopping on and trying to pedal it. If that doesn't work then I'd try tying a heavy weight or looping a paint can around one of the pedals close to the crank.
You're looking for a 7.5 degree distance, so on 185mm cranks that's 24mm or nearly and inch of diference between splines. Weighting the opposite side enough should make it clear. I then took some nail polish and marked both the crank and axle so I didn't have to play this game again.
Some BMX cranks are keyed, so that they will fit only one way. If yours is not keyed, then, no, there is no better way to line it up than to do it by eye.
If you want to double check it, take a plumb bob, and place it across the center of the pedal threads on one crank. Turn the crank until the string lines up with the other pedals' thread center.
If the string follows the center of the crank arms, you are lined up.
As pointed out by @Ehryk, the difference is pretty visually noticeable. Probably not worth all the effort involved here, since you see an almost 1 inch variation by eye easily.
I would try using trial-and-error. First I'd attach one crank arm and get the nut finger tight. Then I'd put the second on where I thought it should be, take it off and put it on one tooth away from that, then try again in the other direction. I can't help but imagine that (as Ehryk mentioned) when it's wrong, it would be very obviously wrong.
Once I was satisfied with that, I'd line up one of the arms with the seat post or the down tube, take a few steps back, and eyeball it.