What type of mortar would I use to seal cracks in our chimney?
Sure sounds like your chimney is a good candidate for a re pointing job. This involves removing all loose and damaged mortar, then pointing all the joints with a portland cement mortar. If you have never done this kind of work, read up on it. It can get quite involved if there are loose bricks etc. It may be a good idea to get a pro, so it will last awhile and not just fall out as soon as it dries. An alternative product for a quick temp fix can be found in a caulking tube. There are several products designed specifically  for masonry and do a pretty good job in sealing small cracks. Remove as much loose mortar as you can to assure the masonry caulk sticks well.