How to cite prices in academia? In the introduction of my thesis I want to motivate the use of alternative neutron converters to helium-3 by mentioning the exploding cost of latter.

I am not directly involved with helium-3, since I work with the alternatives. Online research yielded for instance a congressional research paper by Shea and Morgan from 2010, and the wikipedia page for helium-3 links to an IEEE site also from 2010, mentioning the price explosion in that year.

Is one of those source apt for citation? Is there a best way to cite prices in academia?
There are two, as I see it very different questions you pose. as for the aptness of the sources, the Shea and Morgan paper is a publication that can be referenced because it is traceable and likely to be remaining for a long time in unaltered state. It is also published by a formal body.

When it comes to citing prices the question is perhaps trickier. Not knowing the market for helium-3 I do not know where the prices are determined but usually there is some form of exchange that determines prices based on the market and this makes prices shift quickly. In such cases, one needs to find a source where the market swings are documented and stored so that one can cite a price at a specific time in a time series that people can revisit if they wish to check the correctness of your assessments. This type of referencing is common in economics when discussing price variations, trends etc.