I'd opt for the hotel that's just outside the city centre. You will still be very close, and it's a beautiful walk along the river; the other advantage is that the hotel outside the centre should have better access to parking vs the core, which is like any other European city, with parking space at a premium.

If you're doing day trips...the salt mine in Wieliczka is a must; you can get there via public transit as easily or easier (although not as fast) as driving. Also a day trip to Zakopane (or even an overnighter!) is a highlight of the area; also, east of Zakopane, (I'll find the name of the town) you can go on great river rafting trips along the Dunajec River. Something I didn't get a chance to do when I was there, but the highlight of the trip for my 10 year old son (who went with Grandma) two years ago...

Regards,

John Wiernikowski Hamilton, Ontario CANADA