You can one-time set vars for a single command by putting them on the command line before the command:
$ EC2_HOME=/path/to/dir JAVA_HOME=/other/path ec2-describe-regions
Alternately, you can export them in the environment, in which case they'll be set for all future commands:
$ export EC2_HOME=/path/to/dir
$ export JAVA_HOME=/other/path
$ ec2-describe-regions
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