Through silicon vias (TSVs) provide an efficient way to support vertical communication among different layers of a vertically stacked chip, enabling scalable 3-D networks-on-chip (NoC) architectures. Unfortunately, low TSV yields significantly impact the feasibility of high-bandwidth vertical connectivity. In this paper, we present a semi-automated design flow for 3-D NoCs including a defect-tolerance scheme to increase the global yield of 3-D stacked chips. Starting from an accurate physical and geometrical model of TSVs: 1) we extract a circuit-level model for vertical interconnections; 2) we use it to evaluate the design implications of extending switch architectures with ports in the vertical direction; moreover, 3) we present a defect-tolerance technique for TSV-based multi-bit links through an effective use of redundancy; and finally, 4) we present a design flow allowing for post-layout simulation of NoCs with links in all three physical dimensions. Experimental results show that a 3-D NoC implementation yields around 10% frequency improvement over a 2-D one, thanks to the propagation delay advantage of TSVs and the shorter links. In addition, the adopted fault tolerance scheme demonstrates a significant yield improvement, ranging from 66% to 98%, with a low area cost (20.9% on a vertical link in a NoC switch, which leads a modest 2.1% increase in the total switch area) in 130 nm technology, with minimal impact on very large-scale integrated design and test flows.