Clearinghouse is better because it was co-developed with and runs on VIA, which is now merge mined with LTC.
Counterparty is an unwelcome guest on the Bitcoin ledger. It is considered by many to be spam and/or parasitic.
That is a precarious position; one commit from the BTC core devs can damage or break Counterpary, as can the hostility of pool ops such as LukeJr.