There are several ways to classify position. Sinins' Encyclopedia
does not look at HRs hit while playing a position, it is based on
position played that season. Tom Ruane's analysis of Schmidt is the
most strict way of compiling this information, as he does take into
account the position played at the time the HR was hit.
Others "loose" criteria base it on what a player was known as, e.g.
some still consider ARod a SS, Schmidt clearly was a 3b even though he
played elsewhere, some call Ott a 3b, etc. Personally, I don't like
that criteria, too qualitative for me.

I would suggest going right to the resident expert at SABR: David
Vincent. He has all of this information at his fingertips via SABRs
Home Run Log, updated through 2005 too. He can easily provide the top-
10 HR hitters by all positions, or top-1000, or HRs by position by
league, or HRs by day of the week by LH batters off of RH submarine
pitchers...you get my point.

Incidentally, ARod is close to setting the record for HRs by a SS.
His move to 3b delayed it, but a few more games at SS and he may do
it. Currently, he is at 344, the record is 345 held by Cal Ripken Jr.