In my personal opinion, tomato-shaped pin cushions that are available at the store aren't really that cute. If it only depended on looks, I'd have all homemade pin cushions! However, there is one BIG difference that I'd like to make note of between these two pin cushions. The difference is that the tomato has particles inside which sharpen your pins every time you put them in there, whereas homemade pin cushions cannot provide that luxury!
I'll let you decide what you'd like to do with this information! A good compromise might be to have a tomato as well as a homemade pin cushion (if you have that many pins).