Your choice really depends on your brand. I live in NYC and most of the time that I order food online I just go to Seamless and decide what looks good. There's only been one restaurant that I order from off their own site and that's a pizza place that I love that isn't on Seamless.

If you're a random sushi or Chinese place it's worth the 25% to be in the Seamless directory because otherwise no one will ever order from you. Katz's Deli could probably get away with ordering on their own site because their brand is good enough.