Sampling method decisions are critical for the effective monitoring and management of fisheries. Deploying the most effective sampling methodologies is particularly important when responding to new invasive species, where early response efforts have the best chances for eradication. In the Laurentian Great Lakes, the invasive Grass Carp Ctenopharyngodon idella is sampled using boat electrofishing and the combination method of boat electrofishing within and around a trammel net enclosure. We conducted a field study to compare the effectiveness of the two methods. We used capture data for surrogate taxa (i.e., Common Carp Cyprinus carpio and buffalo Ictiobus spp.) to compare the two methods because few Grass Carp were collected during the study. The sampling methods were compared within an occupancy modeling framework using an information-criteria model selection approach to evaluate seven alternative models. The base model included sampling method, year, water temperature, and sampling effort as covariates in the detection submodel and assumed that occupancy probability was constant across sites. The other six models built on the base model by including site, water body type (i.e., lentic vs. lotic), and interaction covariates in the detection submodel. The top-performing model, built on the base model, accounted for the influence of water body type and assumed the exchangeability of site effects in the detection submodel. The results indicated that the detection probabilities for both taxa were higher for the combination method than for boat electrofishing, with a median estimated difference in detection probability between the two methods of 0.11 (95% CI: 0.04–0.22) for Common Carp and 0.18 (95% CI: 0.08–0.28) for buffalo. Given that the combination method was more effective for detecting the surrogate taxa, we expect the combination method may be preferable to only boat electrofishing for Grass Carp removal.