can i sue a window repair shop that damaged my car due to them not sealing the window down now when it rains inside of my car floods with water

Yes, but you should take a look at the contract you signed with the repair shop.  It is likely that it contains what is known as a "limitation of liability" clause.  Such a provision is likely to provide something along the line of "the repair shop is not liable for any consequential damages resulting from any failure to perform except in the amount of $50."   Such a clause would obviously be a problem for you, but it may not be insuperable.  Courts do not always enforce such clauses, depending on such factors as (a) whether the clause is buried in the small print of a form contract the repair shop has everyone sign, or prominently in a fully negotiated contract; (b) how extreme the limitation is (does it limit liability to $5 or $500) compared to what the reasonably expected damages might be; and (c) other similar factors.