Although it might seem more "authentic" to buy your souvenirs at their source, you can find everything in the city, a real bonus if you're pressed for time. If the capital has any real tourist shopping district, it's found loosely in the cluster of streets around Parque Morazán, just north of downtown, an area bounded roughly by Avenidas 1 and 7 and Calles 5 and 9. Stroll and search, because many other businesses congregate in the area as well.
The northeastern suburb of Moravia has a cluster of high-quality crafts and artisan shops—for good reason very popular with tour groups—in the three blocks heading north from the Colegio María Inmaculada high school. The street is two blocks behind the city's church.
Prices in shops are fixed and fair. You may be able to bargain at Mercado Central and the Calle Nacional de Artesania y Pintura, but bargaining isn’t the sport it is in other countries. Haggling, even if not ill-intended, will come off as rude. Your best bet for getting a deal is to simply suggest you’ll come back later and walk away. If the vendors really want to lower the price, they will.