The best way is to write a JCA adaptor (rar) that adapts between whatever custom mail reading format Lotus supports (assuming the protocol is published etc). The adaptor can then deliver messages using JMS and you can receive them in a Seam managed message driven EJB3. JBoss AS comes with a rar for IMAP and POP3, source can be found in the connector subproject of JBoss AS IIRC.
I had the same Problem,
We have some Data in a Domino Database. For access, I used the Domino ODBC Driver, and the Java ODBC-JDBC Bridge.
It worked realy good. After that I could access the Domino Database the same way I accessed any other JDBC Database.
Hope it helps.