Bone regeneration for replacing and repairing damaged and defective bones in the human body has attracted much attention over the last decade. In this research, highly porous polyetheretherketone (PEEK)/hydroxyapatite (HA) bionanocomposite scaffolds reinforced with carbon fiber (CF) and carbon nanotubes (CNTs) were fabricated, and their structural, mechanical, and biological properties were studied in detail. Salt porogen (200–500 µm size) leaching methods were adapted to produce porous PEEK structures with controlled pore size and distribution, facilitating greater cellular infiltration and biological integration of PEEK composites within patient tissue. In biological tests, nanocomposites proved to be non-toxic and have very good cell viability. In addition, bone marrow cell growth was observed, and PEEK/HA biocomposites with carbon particles showed increased cell attachment over the neat PEEK/HA composites. In cell viability tests, bionanocomposites with 0.5 wt% CNTs established good attachment of cells on disks compared to neat PEEK/HA biocomposites. A similar performance was seen in culture tests of bone marrow cells (osteoblasts and osteoclasts). The 0.5 wt% CF for osteoblasts and 1 wt% CNTs for osteoclasts showed higher cell attachment. The addition of carbon-based nanomaterials into PEEK/HA has been identified as an effective approach to improve cell attachment as well as mechanical and biological properties. With confirmed cell attachment and sustained viability and proliferation of the fabricated PEEK/HA/CNTs, CF bionanocomposites were confirmed to possess excellent biocompatibility and will have potential uses in bone scaffolding and other biomedical applications.