Deals created from the HubSpot Sales Chrome Extension will be created in the default deal pipeline. At this time, we don't have the ability to choose another pipeline directly, but we can change which pipeline is the default, and deals would be created there going forward.
To change which pipeline is set as the default, if we go to Settings > Objects > Deals > Select a Pipeline > Actions > Reorder pipelines, we can move the desired default pipeline to the top and it will be set as the default.
That being said, I definitely understand the validity of choosing the pipeline directly from the extension, and I would highly recommend you post this Idea in the HubSpot Ideas Forum to bring it to the attention of our product team.