Is there a way to transfer money from Dwolla to MtGox without paying BitInstant a 3.99% transaction fee?
Im not aware of a method other then BitInstant with the 3.99% fee.  This can be confirmed at...

https://bitcointalk.org/index.php?topic=160604.0

However, there are other ways to buy bitcoins besides USD deposits to Mt.Gox which may have lower fees.