If USA restrict or put fee on China made ship for port call, then Chine should counter attack by putting free for each Boeing made aeroplane approaching or passing through Chinese sovreign airspace including HK and Macau.
There are many ways to counter the US action, but this action on Boeing is not a good choice because practically every country are using Boeing airlines thus you will hurt enemies, friends and by-standers.
The solutions are many and China can choose one that it deem better suit to their long term strategy. Just like your suggestion on Boeing, the outcome of US action will hurt every body - US, US allies, nuetral countries and countries that oppose US, because China made ship is practially found in every country in the World.
To cut damages from Trump's action, China can designate certain foreign ports as transhipment centres. Chinese made ships can unload their cargo at one of this transhipment ports and then they can delivery the goods to US using any means - by ship/land/air with non-Chinese made transporters .
One such port is the huge port built by China in Peru - the Chancay port. Chancay would become a very busy port for shipment going into and out of US. There are a good number of cargo ships built by South Korea and Japan, they can be used exclusively on Peru-US routes. And Chinese made ships would still sail around the world sans US.