What recipe are you using to make the salsa? Did you add anything acidic, like vinegar or lemon juice? What stuff other than tomatoes did you add? How much of these did you use?
The acid in the mix is what makes it possible to water bath a lot of tomato products. But some tomatoes are not all that acidic, plus to make salsa, you probably added stuff other than tomatoes that may not be all that acidic to start with. When water bath canning tomatoes, tomato juice, puree, or many tomato products, the recipe usually calls for a certain amount of acid, like lemon juice or in the case of salsa vinegar, just to be sure the acid level is high enough. What all this is about is botulism. The botulism organism cannot live and reproduce in stuff that is high acid.
Can you water bath can that salsa after three days? Yes, if the acid level is high enough. I’d boil it for a while before canning it just to make sure it is still sterile. Waterbath canning will not kill all other potential spores and stuff that can ruin it. If you don’t sterilize the salsa and the jars and lids, you might wind up with a mold growing on top when you go to open it.