You need to include the arguments in the Eshell alias as $1, $2, ... or as full list of provided arguments $*. See the documentation of Eshell aliases.
In your special case you could use:
alias cmake 'cmake -DCMAKE_EXPORT_COMPILE_COMMANDS=1 $*'
Have you tried using exec-path-from-shell package? It loads the environment variables that are used in your shell.
If you are using use-package then this should suffice: