I have water seeping into my basement where the mortar has eroded. Is there some sort of waterproofing I can put on before the new mortar, or is there a type of mortar that is waterproof? Any info would be greatly appreciated.
Cement and mortar are not inherently water proof. Water penetration into the basement is probably not the cause of eroded mortar but instead indicative of a more serious problem stemming from the outside.
A complete fix will involve digging up the area outside the foundation, applying proper water proofing, installing weeping tile (or replacing) and drainage, then replacing the soil.
You will probably find that this is not a DIY job.