PS or IS for Piloswine vs. Rayquaza?

Yes

Assuming your charged move is Avalanche, and assuming accuracy in the 'Offensive Moves Explanation' on the Piloswine page, there is an essentially negligible difference between the DPS of these two quick moves.

Against Rayquaza, Piloswine with 15 Atk (14A) reaches its final breakpoints for both moves at L31.5 (L32). For second-highest breakpoints, you are looking at 15A L26.5 for Ice Shard, and 15A L23 for Powder Snow. Assuming your aim is to hit the highest breakpoint, there are no differences in the candy/dust investment required for these moves.

Taken together, this suggests that there is a very minor difference between using IS and PS for Rayq.

The difference is small but pokebattler seems to favor IS in most cases, giving it 2-4% better time to win. I've TM'd mine to IS because I have too many of them, but I would not worry about which one is better, unlikely to make any kind of a difference.

IS

Evaluated over time, they are both about equal, but Ray chews through Piloswine rapidly, so you'll want to get off as many Avalanche as you can in that time. Powder Snow does that job a lot better with its incredible energy generation.