Ok, so allow me to fully clarify this for everybody.
You can replay the last level a few times to help get this, as you get something like 20-30 extra lives after beating the last boss (I dunno the exact amount), but the achievement WON'T unlock if you reach 99 lives this way.
You MUST collect an extra life token in order for the game to officially register your 99 lives.
I reached 99 lives after doing the last level for the 4th time, and didn't get the achievement until I died while replaying the first level and gained an extra life afterwards (as commented by Efford on one of the other solutions).
Whilst I realise this has already been pointed out, the purpose of writing this solution is to make easily, and instantly, noted to anyone who has encountered the same issue.
I hope this clears up everything.