soft margin SVM would be useful here. And there are manifold aware topographical clustering algorithms, like Persistent Homology techniques, Gunnar Carlson is the man on this new clustering offshoot.
Oddly enough HDBSCAN can be recast as a persistent homology computation; the trick is in simplicial complex construction; you need something slightly more density aware than traditional Rips complexes. I am currently working on designing a version of Carlsson and Memoli's Multiparameter Hierarchical Clustering based on the persistent homology interpretation of HDBSCAN.
