Sometimes we can get so wrapped up in the coolest tools to do alignments that we miss the most basic. A good GPS tool (garmin handheld, etc), a calibrated compass, and a declinomenter (from Home Depot or Lowes) are as good as I've ever really needed to align antennas out to a few miles. The antennas we're working with have 10-30deg beam widths, and when stretched out over a mile have pretty good leeway. If you are trying to the absolute edge and trying to find that last bit of max gain between the 3dB spread, then you can look at purchasing some of those digial laser/reflective solutions that cost thousands of dollars, that are used to align laser comms systems and the like.
I know some of our (Aruba's) guys have built some laser-rigged contraptions. The trick is to make sure that your laser system is adjustable with regard to the mechanical source plane, since many antennas have some degree of electrical downtilt or uptilt. So if you make something with a flat back to clamp on to an antenna and make your laser 90deg perpendicular to the plane of the physical antennas, your laser may not be at the actual max peak. It may be 2-7 deg above or below the plane.
Just something to keep in mind.