As of June 1, 2015, the IDE Connector documentation will no longer be maintained by Atlassian. See https://developer.atlassian.com/blog/2015/06/discontinuing-ide-connectors-support/ for more information. We will also be making this documentation available for our open source community here: http://atlassian-docs.bitbucket.org/
NTLM support is limited by the libraries that Mylyn uses for network communication. A suggestion is to take a look at the NTLM authorization proxy, which has been reported to work with the Mylyn JIRA connector.