I'm from NY and got my undergrad from a SUNY. I would say as far as reputation goes, Stonybrook has a better one in terms of sciences. However, Albany isn't too far behind. Albany is good if you want to stay in the area- the nanotechnology/science field is really up and coming in Albany. I would say Stonybrook would have a more far-reaching reputation.
Personally, the financial situation and research situation at Albany would scare me. At the school I'm committing too, I have five options of PIs. Two seems like it's cutting it close. However, I think it's really up to you whether doing your first choice research is worth that risk. You seem fairly insterested in the Stonybrook research- maybe email a few PIs to see? Or look into if there are some PIs at Albany doing your secondary interest?
Let me know if you have any more questions! I grew up in the Albany area.