I doubt that the German Navy could count on the Luftwaffe for much of anything in the 1940 timeframe. The Luftwaffe had given no, none, nada, consideration to the maritime patrol naval attack role for their aircraft. Outside a handful of Küstenflieger gruppen that were primarily for coastal patrol in near waters no units existed for this type of work.
The handful of Fw 200C that existed and were pressed into this role proved extremely unreliable. It wouldn't be until late 1940 that even a handful of dedicated aircraft became available for maritime patrol. Even then, their operations were made completely independent of naval operations. Their support of U-boat operations was far more incidential than planned when it did occur.
Outside the Fw 200 the Luftwaffe also lacked any really suitable long-range bombers for maritime patrol or attack. Certainly neither the Ju 88 of He 111 could operate out into the Atlantic. So, the question is what aircraft do the Germans use to attack convoys? Even the Fw 200 attacked shipping close to England or Ireland on the occasions when they did.

Now, on the Thames thin: Even in 1940 the British had CD radar stations covering this estuary and most of the Southern England coast. The approach of Geman capital ships would be seen on these radars and allow coastal defense batteries plenty of time to respond.