Ferrara proved his mainstream mettle in an association with TV producer Michael Mann, beginning with his direction of two episodes during the first season (1984-85) of NBC's "Miami Vice", which led to his helming the critically-acclaimed two-hour pilot of "Crime Story" (NBC, 1986). Although Ferrara's wife Nancy walked out on the premiere of "King of New York" (1990) because of its treatment of women, the film attracted more interest than any of his features to that time, helped by the presence of screen heavyweights Christopher Walken, Wesley Snipes and Laurence Fishburne. 1992 marked the release of Ferrara's ambitious "Bad Lieutenant", starring Harvey Keitel in a tour de force performance in this relentless character study of a disillusioned NYC cop descending into a colorful hell of drugs, alcohol, and corruption when the brutal rape of a nun forces him to confront personal issues of faith and redemption. Long-time writing partner St. John, a devout Catholic, refused to work with Ferrara on the picture due to its blasphemous images but was back on board for the next four flicks.

For his next two films, Ferrara found himself out of low-budget waters for the first time. Madonna's $4 million salary alone for 1993's "Dangerous Game" (originally given the more interesting title "Snake Eyes") could have financed two Ferrara films and swelled the budget to $12 million. An unconventional account of the process of filmmaking, also starring Keitel and James Russo, it received decidedly mixed reviews, but at least it got a wide release. His sci-fi thriller, "Bodysnatchers" (1994), the second remake of Don Siegel's 1956 classic "Invasion of the Body Snatchers", suffered inexplicably at the hands of Warner Brothers. Although favorably reviewed at several major film festivals, the studio mysteriously shelved it for a time and marketed it pitifully upon its release. Consequently, the $20 million picture did relatively little business when finally exhibited and helped make Ferrara an even more resolute independent filmmaker and foe of the studios.

Refusing to be compromised by money matters, Ferrara returned to the low-budget viscerality of his early work with "The Addiction" (1995), on the surface a tale of vampirism. Filmed in black and white, it is really a theological tale probing the corrupt human condition while allowing Lili Taylor's character a way out through Jesus Christ. He continued in the same vein with the 1930's gangster piece "The Funeral" (1996). Christopher Walken, the oldest of three brothers, wrestles with a Catholic conscience at odds with his need to revenge his younger brother's death. Chris Penn turned in a riveting portrayal of the insane middle brother and Isabella Rossellini, Annabella Sciorra, Vincent Gallo and Benicio del Toro all contributed notable performances to a movie of hypnotic intensity rooted in the behavioral nuances of the characters. For "The Blackout" (1997), Ferrara temporarily abandoned his usual NYC locale for a warmer Miami but returned to New York where Matthew Modine, comfortably settled in domestic stability with his girlfriend Claudia Schiffer, must confront the trace memories of a murder he committed during an alcoholic blackout 18 months before in Miami.