Generally, using S3 filesystem in EMR with Flink has worked pretty well for me in Flink < 1.2 (unless you run out of connections in your HTTP pool). When you say, "using Hadoop File System class", what do you mean? In my experience, it's sufficient to just use the "s3://" filesystem protocol and Flink's Hadoop integration (plus S3 filesystem classes provided by EMR) will do the right thing.
-Shannon
