Today it would be impermissible. When a person says Allah taala knows best it means that concerning a particular issue his knowledge is perfect as He is the All-knowing. The same cannot be said about the Messenger of Allah, peace and blessings upon him. This phrase was said by some Sahabah, such as Umar r.a. in the Hadith of Gibril, however that was possible then by virtue of the Prophet, peace and blessings, having revelation. Having said this, it is still permitted to say the phrase by way of narrating a hadith that has this phrase.