HKDF entropy extraction
Yes, that should be secure. It seems however that your problem lies with the secure random number generator and that you are using a KDF to overcome those. Basically you are using a KDF as key generator; no keys are derived from another / master key.

It seems more obvious to use a DRBG / CPRNG (deterministic random bit generator / cryptographically secure pseudo random number generator - there are probably more names) and seed it with random values from the system and the user. After that you can just extract the key bytes, and you would still be left with a (fast) RNG that you can reuse / reseed - something you will likely need later on.

Many API's already provide these out of the box, and usually they are pre-seeded as well, so you may just have to add your user generated entropy to the state by mixing in additional seed data. Nothing stops you from adding HKDF + OtherInfo in addition to the DRBG of course, but that is not required.