In terms of trust, there is no denying that you need to trust Whirlwind more since you need to deposit coins to their service, as opposed to Whirlpool where you stay in custody of your coins. There is also the issue of trusting the service not to log what you are doing, which can be prevented with Whirlpool by using your own node and Tor.

In terms of privacy to an outside observer, then at the moment it depends on how you use them, but in the future I would say Whirlwind will provide better privacy than Whirlpool. If you coinjoin on Whirlpool, then your privacy is dependent on how many times you let the coins be mixed before you spend them. Assuming 5-input and 5-output coinjoins, then after one mix your backwards looking anonymity set is a maximum of 5. After two mixes, a maximum of 25. After three mixes, a maximum of 125. And so on. I say maximum, because if other people in the coinjoin do something stupid and deanonymize their coins, than that lowers your anonymity set. If you leave your coins in Whirlpool for months and months and end up with 10+ remixes then that's a very good anonymity set, but if you just let them be coinjoined once or twice before you spend them then that's not a very good anonymity set. This same principle applies to any coinjoin implementation. Whirlwind, on the other hand, currently has an anonymity set of 414 as long as you don't deposit huge amounts, and this is only going to grow. In the future, you will be able to get an anonymity set with Whirlpool of 10,000 or more.