John Lawler asks the right question in the comments - is it the study of hidden [alien biology], or is is the study of the [biology of hidden things] that are alien?
If it is the study of hidden alien biology, then you should use cryptoxenobiology, where crypto- describes the particular kind of xenobiology (alien biology). For example, if we suspect that a lifeform from Delta Crateris has burrowed into the Gobi Desert and is cohabiting with the Mongolian death worm, the study of that lifeform would be called cryptoxenobiology, since the lifeform is not just alien, but also in hiding.
If it is the study of the biology of hidden things that are alien, then you should use xenocryptobiology, where xeno- describes the particular kind of cryptobiology (biology of things that are hidden). For example, if we are in contact with an alien civilization from Gamma Vulpeculae, and they ask us to study reports of a strange creature that lurks in their forests much like Bigfoot allegedly does in ours, the study of that strange creature would be called xenocryptobiology. To the Vulpeculans, it would be cryptobiology, but since to us it's an alien, we'd put our xenocryptobiologists on the case.
In this particular case, the two interpretations are really very close, and I suspect that either one would be okay for whatever purpose you have in mind, particularly since neither of those words sees any use whatsoever.
"Antidisestablishmentarianism" is the position opposed to (i.e. anti-) disestablishmentarianism, which is the idea that church and state ought to be separated ("disestablished"). "Disantiestablishmentarianism" would, I guess, be something like "the position that those who are antiestablishment must be brought down", which is a very different thing.
Similarly, "unpremeditated" means "not (i.e. un-) premeditated", whereas "preunmeditated" would mean something like "not meditated upon, and the non-meditation was done in advance" (which doesn't make any sense, at least to me).
In general, the idea is that you build from the root word outwards. Start with "meditated", which means "planned" in this context. Then add the next-most-inner affix pre-, and you get "premeditated", which means "[planned] in advance". Finally, add the outermost affix, and you get "unpremeditated", which means "not [[planned] in advance]".