i live in zurich and i'm happy here paddling wise, although for me, basel would be a bit better, because i would then be paddling in huningue a lot, but maybe that's just me. others would find huningue boring after a week or so.
as for the alpine rivers near interlaken/bern, those are about the same distance from basel and zurich.
zurich is closer to bremgarten, and to the rivers in central switzerland, graubuenden, austria, ticino, and the italian alps. let's say, on average, 45 car-minutes closer.
on the other hand, basel is a bit closer to the rivers in the german black forest and the jura. those rivers are very much rain depending though (black forest mostly runs in winter), so that's a personal preference.
basel is not a boring city. being right next to germany and france gives the city a very open and international touch. and the old town is a lot nicer than you may think after your first drive-thru on the freeway. although the old town of zurich is definitely even more beautiful, and you'll typically find a bit more nightlife in zurich too if that's your thing, but again, there is quite a bit of that in basel too.
practical tip: avoid speaking high-german. either learn some swiss german or speak high german with a heavy dutch or english accent. it will make the people you meet so much more friendly.
enjoy switzerland, it's a great place to live, regardless of which city...