An overall reddish tone, including the tail, is pretty common for chipmunks. I haven't paid attention to where and when, but it does vary. I would guess that they look a bit greyer in the winter and redder in the spring.
In the northeastern US, there is only one species of chipmunk: the Eastern. If you see a small rodent with bold white stripes running down its upper flanks, it's an eastern chipmunk (in the eastern US).
Red Squirrels are slightly larger, furrier tailed, and redder. Less likely to spend time on the ground, and got no stripes.
The Eastern grey squirrel - no risk of confusion there.
Woodchuck - even less.
You're not likely to actually see a flying squirrel, at least not in the daylight. That completes our list of sciurids in New York and New England.
"Some were quite large" - Either you saw a mix of red squirrels and chipmunks, or you caught a brood of young chipmunks in the first few days after they left the nest. The timing is a bit early, but not impossible. (Normally born May or June, emerge at least a month later.) You'd see 2 to 7 small ones per 2 adults, and you'd only be likely to see one family at a time.
A hybrid between a chipmunk and a red squirrel would be extremely unlikely. They're in different genera.
