First, alignment does not cause vibration.
Sometimes the person(s) balancing the tires needs to be shot. I've seen so many balance problems occur due to operator error in just mounting the tire to the balancer. A lot of wheels require that the wheel be 'back-coned' when mounted on the balancer. But, for some reason, most guys will slap the wheel on the balancer then place the cone on from the front side of the wheel. This many times does not properly center the wheel on the balance arbor and will cause the wheel to spin off center.
Beyond that, you should seek out this balancer:
http://www.gsp9700.com/pub/search/FindGSP9700.cfm
It applies 1000 lb. against the tread of the tire and spins it slowly, measuring deflection against the drive roller. If the tire/wheel combination has excessive 'road force' issues it will direct the operator to measure the wheel run-out. After that is done it will provide tow positions, one for the tire and one for the wheel. The operator then deflates the tire, breaks the bead loose and aligns the two marks. This will place the tire/wheel in its best position for road force run-out. After this is done the tire/wheel is placed back on the balancer for final balancing.
Note: normally the balancer considers 30 lbs. or less to be acceptable. Don't let them get away with that. Shoot for 15 lbs or less, under ten is great!
This type of balancing costs more (probably figure around $75 for 4 tires) but the results are fantastic. I do this stuff for a living, and have for more years than I care to admit. The process is a bit labor intensive but you get more for your money than you would with a 20 second per tire balance.