Honestly, I don't think it's a big difference. DCA and PHL are close enough that the weather is probably going to be the same in both places. You're on a CRJ from YYZ to both, so no difference there...I probably would pick PHL simply because there are more daily flights between YYZ and ISP, so if something goes wrong, you'll have more options...
Yes (depending where on Long Island and how you want to get to the airport), but far fewer flight options.
The further east you are the less the difference between JFK and LGA. I live a mile off the LIE just over the Nassau/Suffolk border and the two are about equidistant, or at least within a mile or two of each other. That said, ISP is MUCH closer, only about 20 minutes away.
Depends what FF program you're putting the miles into. US only gives actual miles flown on flights under 500 miles in other FF programs like UA/MP, even if you are elite in that program. Discovered this the hard way when my segment from EWR-PHL posted as 86 miles (or something similar). So I'd suggest flying via DCA if depositing miles into UA/MP or AC/AE. Also, PHL is an awful airport to connect through if your flight arrives at the commuter terminal and departs from the main US terminal area (though assume both flights would be in the commuter terminal). Still DCA is a nicer airport with a nicer club lounge.