It's really up to you where you take it. I felt that I learned much better at the CC when I took Ochem because of the small class size, 14 compared to 400 at my university, and that my professor was actually a very dedicated teacher, not a researcher who may not be the best teacher - and I've run into many, especially since I go to a research school.
As stated above, weigh your options. Find out about the teachers on sites like ratemyprofessor, etc, or if you have friends who've taken Ochem from some of those professors. If you do take Ochem at the CC, you'll really need to show the Adcoms that you can not only pass your upper division classes, but do WELL in them - that will show them that it wasn't just the CC that you went to, but actually you who's good. Also, as pointed out, some schools have restrictions on CC pre-reqs, but I found that often they can be more of guidelines than hard rules, as I got into a school that claims they don't take CC pre-reqs when I took Bio I/II, Ochem, Gchem, and Physics at the CC. It also didn't come up at any of my interviews either - but that's just my experience.
I'd say that if you had to wait a year to transfer just so that you could finish the Ochem, I'd start the Ochem at the University if it would let you graduate sooner, but again, just do what you feel works best for you.
Good luck, and I hope this helps.