I was in the same position as you a couple of years ago and did a lot of research into this issue. In a nutshell, unfortunately, it is true that CC grades are not percieved as competetive as University grades. Thus, it is recommended to take your sciences at a 4 year school.
However, if you plan on taking upper level courses at a 4 year school in the same area as the introductory level course you took at the CC then it shouldn't pose a problem - assuming you do well in them of course. In my situation I took my intro biology and chemistry courses at the CC because I knew that I would take quite a bit of upper level bio and chem courses (Biochem Major) at my 4 year school. I avoided physics at the CC for the same reason, I wasn't planning on taking any upper level physics courses. I was also told to look at Orgo as a seperate discipline as well, if you don't plan on taking advanced organic chemistry at a 4 year school (some schools don't even offer this to undergraduates) then avoid taking orgo at the CC as well.
Hope this helps...