Choice of cultivar, training system, planting density, and rootstock affect orchard performance and profitability. To provide guidance to growers in northern cold climates on these choices, a field trial was established in Peru, Clinton County, NY, in 2002, with two apple cultivars (Honeycrisp and McIntosh). From 2002 through 2016, we compared Central Leader on ‘M.M.111’; Slender Pyramid on ‘M.26’ and ‘Geneva® 30’ (‘G.30’); Vertical Axis on ‘M.9 (Nic® 29)’ (‘M.9’), ‘Budagovsky 9’ (‘B.9’), and ‘G.16’; SolAxe on ‘M.9’, ‘B.9’, and ‘G.16’; and Tall Spindle on ‘M.9’, ‘B.9’, and ‘G.16’. Central Leader was planted at 539 trees/ha, Slender Pyramid at 1097 trees/ha, Vertical Axis and SolAxe at 1794 trees/ha, and Tall Spindle at 3230 trees/ha. Cumulative yield was higher with ‘McIntosh’ than with ‘Honeycrisp’. High planting densities (Tall Spindle) gave the highest cumulative yields (593 t·ha−1 on ‘McIntosh’ and 341 t·ha−1 on ‘Honeycrisp’). Tall Spindle (3230 trees/ha) on ‘M.9’ appeared to be the best option for ‘McIntosh’. On the other hand, for a weak-growing cultivar such as ‘Honeycrisp’, Tall Spindle on ‘B.9’ (366 t·ha−1) and Slender Pyramid (1097 trees/ha) on ‘G.30’ (354 t·ha−1) were the two combinations with the highest cumulative yield, largest fruit size (220–235 g), and greatest efficiency index (4.6–3.9 kg·cm−2).