Does it look bad to have only 3 years of science?

You do have one each of biology, chemistry, and physics, which is the best possible three years of science. It will probably look better to take a four year (a more advanced course in one of the three), but your science courses probably look better than those of someone who took three or four years of science but skipped one of the three primary ones. If you intend to major in any kind of science, taking an additional advanced level science in high school (if available) would be more strongly recommended.

What the colleges you list say:

Bowdoin at https://www.bowdoin.edu/admissions/apply/selection-process.shtml : “Although Bowdoin does not require a prescribed high school program or number of courses, the typical entering first-year student will have had four years each of English, foreign language, mathematics, social science and three to four years of laboratory sciences.”

Williams at http://admission.williams.edu/apply/ : “Applicants to Williams should pursue the strongest program of study offered by their secondary schools. While there are no absolute requirements for admission, competitive candidates typically study English, math, natural science, foreign language and social studies in four-year sequences and present a distinguished record throughout their secondary school career.”

Brown at http://www.brown.edu/about/administration/institutional-research/sites/brown.edu.about.administration.institutional-research/files/uploads/CDS_2014-2015.pdf : 3 science required, 4 recommended in section C5.