The nicest, most ordinary couple in manga is Shiro-Kenji in What Did You Eat Yesterday?
What makes them so nice is that they aren't super-perfect nice. They don't bring flowers and puppies into every encounter. They are, in fact, incredibly normal. Shiro is a tad self-centered and stuffy. Kenji is a little flaky.
Consequently, the sweet moments are sweet without being saccharine: Shiro gets peaches for Kenji; he worries when Kenji doesn't pick up the phone immediately; he decides to spend all his New Years with Kenji.
Kenji naturally and pleasantly does housework. He compliments Shiro's cooking without pause. He knows when not to tease Shiro too far.
Regarding other manga: many of Yugi Yamada's characters are also simply and normally nice--she creates full worlds of friends and family members and relations.