I'm in the same boat in Ottawa. Many Canadians have gone on to work for startups in the US. What I've always seen, from friends and family who've been down this road, is that US companies (big or small) wanting to hire Canadians have always been very helpful in the visa process. Of course, your mileage may vary.
I think your best bet is to throw your resume in, clearly indicating your current location.
Problem is, I'm in Toronto and only through a NAFTA VISA I can work there. I highly doubt many of the jobs are open to this Visa. That's frustrating.