Hisat2 is more recent, a bit more efficient, and have more features including soft-clipping and spliced read alignments. With eukaryotic RNA-seq data, Hisat2 is vastly superior to bowtie2 because it will be able to deal with introns. With DNA-seq data (or RNA-seq in a species with no intron), you can use either of them, although some might prefer Hisat2 because it is more recent.