I've seen RDS have significant per-query overhead, and some very, very variable read times - in particular, some simple SELECTs randomly taking > 10s every so often.
RDS is subject to the exact same intra-region latency issues that other AWS instances have. Perhaps worse in some cases, since their failover appears to be DRBD based.
Is your ec2 instance in the exact same zone/region as your rds instance? An ec2 instance in us-east-1a will have extra latency dealing with an instance in any other zone, even us-east-1c.
Stating us-east-1a means nothing, since your us-east-1a is someone else's us-east-1d. They're not the same across AWS accounts.