I'm wondering if I correctly understand what is giving you trouble.
You can re-apply the old surface name to the fin by reselecting the polys and picking the previous surface name. So if you are using a surface named "body" and a surface named "fin", while in poloygon mode, press "w", pick the surface named "fin" from the Surf: dropdown list. Click the + button next to Surf: then assign the "body" surface by pressing "q" and picking "body" from the dropdown list.
Then you would apply your gradient to the "body" surface.
You can leave the fin surface if you like and apply the gradient, as well as other surface settings, to both the fin and body.
Hope this helps.