all the hotels near wrigley field are crappy. Just stay in the loop or the gold coast. The ballpark is just a cab/subway ride away. with the subway, you can take the red or brown line right to the ballpark
Six flags is about 45 minutes north from downtown, there's a pretty big shopping mall called gurnee mills right down the street from six flags.
Best thing for tourists is to check out the site
www.metromix.com it has pretty much everything you need to know about in chicago.