Kim, all good questions ... I'm just tossing out a few thoughts here, and welcome others who want to tell me that I'm w- w- wrong.
First, since Manhattan clam chowder is what I'd call diner food (in a good way!) as opposed to fancy food, I think chopped canned clams would be fine. I've used the small cans from Lotsa Pasta for linguine with white clam sauce, and they're fine.
For tomatoes, definitely canned in winter, and for cooking in general, I like starting with whole peeled and chopping or smooshing as I need it. We love Red Gold brand, which is not at all artisanal but a regional (Northern Indiana) company that has always satisfied me. Always in stock at Kroger.
Good luck! Let us know how it goes.