My husband and I replaced the brick of our fireplace, we ended up going with a brick/stone veneer. Because of availability and price we had two options, unfortunately after it was compleat I decided I don't like the color on some of the stones. The main is color cream or beige but some pieces have a darker grey and a red tone. To me the red looks pink and the grey is more of a blue so I want to get rid of those tones. I had an idea to use some type of paint to stipple in to those particular spots but not sure what product to use or what tool/ brush would be appropriate. Please help!

Your surely going tocome to regrete trying to do that.
Once it started there's no going back.
Once it hits the brick it gets soaked into the pores and is all but impossible to get off and will end up have to paint the whole thing one color.

I'll give an alternate answer, although the 'best' solution will be to re-do the brick veneer in a different color pattern. If you can accept the fact that you'll likely have to re-do the brick, then you have nothing to loose by trying to paint. Try finding some Fleck-Stone spray paint in colors similar to what you are looking for - get several different colors. Tape off the mortar joints around the bricks you want to paint to keep the paint out of the mortar. Then LIGHTLY spray paint the brick. Do just a little at a time to keep the coats thin and avoid paint runs. Plus, thin coats will make for a more natural feathering effect and look more like the other bricks.

Depending on the varied colors of the brick you have now and what colors you will be happy with, I'd give this maybe a 25% chance of working. If it works, then you have found an easy solution. If it doesn't, then pry off the bricks you hate and install more.