I dropped a heavy shelf on top of foot 3 weeks ago. Xray at time was normal. But still hav extreme pain when I press on one spot on top of metatarsal?

May want repeat xray. It is possible to have significant pain due to soft tissue injury alone. It is also not so uncommon for very subtle, or non-displaced fractures, to not be detected initially on x-rays. You may want to have an x-ray repeated if your suspicion is still high. Other imaging studies such as MRI, CT or bone scan also may pick up subtle fractures missed by x-ray though they may not be cost effective.
Time will tell. If it is in only one spot and hurts only to press on it, then, I would leave it go for a few weeks more. It would be more concerning if you had pain when you put pressure on it by way of standing. Three weeks, simply, may not be enough time for complete resolution. I would expect, however, that degree of discomfort should be reducing as time passes.