I wonder what that other factor could be?

Maybe people living in abject conditions in the street and defecating in the open? Just a hunch.

Obviously homelessness is the core issue, but unfortunately most countries let people live in those conditions. Nonetheless, there was no outbreaks like the one mentioned in the article in other places banning plastic bags. So assuming that there will be the same sad consequences in New York is just wrong. It would be great that nobody had to leave in street, but in the current situation there must be something specific in San Diego that caused the outbreak, and it's obviously not just banning plastic bags.

This is anecdotal, but having lived on both coasts, public defecation is not nearly as prevalent on the East Coast.

New York doesn't have a public bathroom system per se, but government offices like libraries are extremely prevalent, and those will have public bathrooms. Some stores also have bathrooms that are more or less open to the public.

US cities in my experience have very few public toilets. The only exceptions I can think of are the ones in parks & beaches.