Can I apply for a U-visa, even though I entered the US with a C1/D crewman visa?

Yes. Provided you meet all the requirements of a U visa, the entry on a C1/D visa would not be the basis for denial. It can sometimes be tricky as to whether or not you entered on the C or D part of the C1/D and depending on the answer you may need to file for a waiver of inadmissibilty but either way this entry should not create a denial for your U visa. Given both the complex nature of U visas AND the your less common entry you should definitely speak to an immigration attorney before moving forward. Also, without a full consultation the majority of advice you can find online will be speculative of your circumstances. Best of luck!