You might want to get in contacy with a realtor because some almost all of the apartments within both areas are not openly advertised. For example, the East End is full of apartment buildings owned by single families.
Do you have a car? I would recommend either one, but if had to pick between the two would do downtown. Walking would be a huge advantage, and there are alot of great stores and restaurants right there on Capitol St. But the East End has alot to offer to.
Have you visited before?