Greetings,
Generally, only components such as drivers or RTEs are available as standalone .EXEs, but they generally will be Window's Installer based also (here's the CVI 6.0 RTE as a setup.exe: http://digital.ni.com/softlib.nsf/websearch/56E74D08EFDEFE2386256AE700639CB9?opendocument&node=132070_US).
In your case, the best option would probably be to build a distribution kit will all of the options you wanted (RTE, NI-Reports, etc). Then, call this distribution kit setup.exe from your third-party installer (most installer technologies can do this). Also, you can pass a /Q to the distribution kit setup.exe, which will turn off all of the dialogs and make the install silent.
Hope this helps,
- WesW / NI