The easiest solution would be to put a lifter on one binding and none on the other. The only downside is that he would always have to use that particular ski on that particular leg, but as long as he's good with tuning (or having the skis tuned) that's not such a problem.
A slightly more complicated solution would be to build up the sole of the appropriate boot. This involves having someone who is very experienced in re-working soles as the boot needs to still meet DIN specifications after the work is done (so the binding still works correctly). Probably the only person in the east that I would trust to do this kind of modification is PJ at Racestocksports.com (he's located in Waterbury, Vermont, just north of Sugarbush and south of Stowe). He mods quite a few boots for racers in this manner.
For shops in NYC, try Pedigree. The guys I know from there are usually up for a challenge. See if Jeff is available (manager).