Are Rivers and Aquifers guaranteed to come together in Dwarf Fortress?

No, they're not guaranteed to come together, at least not when considering a brook the same as a river. A brook is easier for beginners to start with, and has the same benefits as a river.

I usually use the following settings in the find dialog to find a good place for starters:

• Evil: Medium
• Temperature: Medium
• Rain: Medium
• Flux Stone: Yes
• Aquifer: No
• River: Yes

You might also want to read my reponse on the question for a good starting location for beginners.

I know you can find brooks in areas that do not also have aquifers. In fact, brooks are easier to work with because they can be walked over, so I really recommend them over rivers for starting with.

If you can't find a good starting area (there's a lot of places to look, don't give up too soon!) you might have generated a difficult world. You can always regenerate.