There is a web interface for the Verbmobil corpus that may give a rough approximation of what you need. Try the query [lemma="kommen"] []{0,10} auf for forms of the word aufkommen in which the auf is separated by up to ten words.
This is of course suboptimal; you really want to find examples in which kommen and auf are in a specific syntactic relationship. But to find examples like that, you'd need (a) a parsed corpus, and (b) a search language that can describe syntactic patterns and not just surface word order. If you wanted to go down that rabbit hole, I'd suggest the TIGER corpus, but it's not web accessible and not really usable by people who don't understand a bit about linguistics.
As Mitch points out in his comment, the separable prefixes are an unusually tough case. So comparing counts for kommen and aufkommen will actually be much more difficult than doing other sorts of comparisons. If you wanted to know something like "Is kommen (with or without a prefix) more common than gehen (with or without a prefix)," you could get a pretty good answer from Verbmobil. You need to use the advanced search so you can set the number of returned matches above 100, but if you do that, [lemma="kommen"] gives 1176 matches and [lemma="gehen"] gives 4545.
(Those counts also highlight another disadvantage of the Verbmobil corpus: it's much smaller than Google's. This is generally true in corpus linguistics: it's easy to get enormous corpora of raw text, but corpora with any sort of grammatical information attached are really labor-intensive and tend to be much smaller.)