The code allows a few options here.
Bond at the Transformer
Bond at the first panel/disconnect
Part of 250.30(A)(1)
this connection shall be made at any point on the separately derived system from the source to the first system disconnecting means or overcurrent device,
Bond at both places if this will not create a parallel path.
Part of Exception 1 to 250.30(A)(1)
A bonding jumper at both the source and the first disconnecting means shall be permitted where doing so does not establish a parallel path for the grounded circuit conductor.
From your description you will have a parallel path (the grounding conductor and maybe the raceways) if you bond at both.
I bond at the transformer and never again, it is a policy of the company I work for.
[This message has been edited by iwire (edited 03-19-2004).]