Writersoul actually gave me an idea – It could be that the map didn’t actually show transformed animagi, like it didn’t show people under the Polyjuice Potion, and thats why Fred and George and Harry didn’t notice Wormtail.
Lupin, however, was one of the creators of the map. He might have been able to use it in ways nobody else could. I imagine there was a way of activating it to show animagi, and Lupin did just that. Remember, Lupin was using the map because he thought they might go to Hagrids, and therefore wanted to make sure nothing happened to them. Knowing as he did that Sirius was a animagus, he would have activated it to check if Sirius was anywhere on site. Suddenly, he saw Peter Pettigrew as well. You could also say, a slight variation of this, that even though general animagi would show up, the Marauders coded that map to show nobody but a fellow Marauder their own animagi, because their animagi were illegal and secret!