I'd love to see a different part to Chicago than just downtown, Oakbrook and the airport so I was thinking of visiting a suburb like Naperville or Lisle. Anyone know if that's a no no or if there's anywhere else that might be worth a visit?

Deep Chicagoland Suburbia. IMO there isn't anything to 'see' in those areas. Family burbs with malls.  
If you've been downtown and O Hare area why not get yourself a nice air B& B in one of Chicago's  neighborhoods?  Andersonville, Bucktown, Lincoln Square much more to see, do and walk to when you have downtime.  Cafes, independent artist, music, cuisine of all sorts, boutiques.  
There isn't anything wrong with both the areas you mentioned but definitely not anything interesting.

I am not sure about the SW burbs, I don't hear about a lot going on there. And, I know for a fact that Naperville has a heavy LE presence.

Yes. That sounds like a great idea. Maybe travel to Milwaukee to check out the breweries?

Chicago has great breweries, but yes we smuggle New Glarus back every time we cross the boarder ; )

There's only so much window shopping I can cope with on the Mag Mile !!!!

That would be Tinley/Orland Park, or in the extreme Bolingbrook/Romeoville.