Does "market manipulation" apply to Bitcoin and other cryptocurrencies?

Yes. It applies to securities through section 9(a)(2) of the securities act, to commodities like bitcoin through 13(a)(2) of the commodities act, and everything else through broad, generic Federal fraud statutes.

"It shall be a felony punishable by a fine of not more than $1,000,000 or imprisonment for not more than 10 years, or both, together with the costs of prosecution, for: .. Any person to manipulate or attempt to manipulate the price of any commodity in interstate commerce ... or knowingly to deliver or cause to be delivered for transmission through ... means of communication false or misleading or knowingly inaccurate reports ... that affect or tend to affect the price of any commodity in interstate commerce[.]" -- 7 USC 13(a)(2)