Neither Sadiq Khan nor any other Mayor of the past or near future is, in reality, boss of the Metropolitan Police. The Commissioner is their boss, and he/she is appointed by the Home Secretary, admittedly in consultation with the Mayor: there is no guarantee that, in the view of disagreement, the Home Secretary's favoured candidate will not prevail, and this may have happened in the case of the present incumbent.
The Commissioner is accountable in law for exercising police powers and is held to account for the delivery of policing by both the Home Secretary and the Mayor. The Home Secretary is specifically responsible too for the Met's counter-terrorism and other national policing matters entrusted to them, with the Mayor playing no part in these.
In short, London's elected Mayor's real powers are piffling compared to other cities worldwide, particularly as their tax-raising powers are so limited. Blair and Brown made sure that Prescott's obsession didn't achieve much so as to keep Ken Livingstone and his ilk in check.